One goal of the Section on Drosophila Gene Regulation is to understand the regulation of homeotic gene function in Drosophila. The homeotic genes encode homeodomain-containing transcription factors that control cell fates by regulating the transcription of downstream target genes. The homeotic genes are expressed in precise spatial patterns that are crucial for the proper determination of segmental identities. Cis-acting transcriptional regulatory elements from the homeotic genes have been previously-identified by assays in transgenes in Drosophila. These assays have identified both tissue-specific enhancer elements, as well as cis-regulatory elements that are required for the maintenance of activation or repression throughout development. While these transgene assays have been important in defining the structure of the cis-regulatory elements and identifying trans-acting factors that bind them, their functions within the contexts of the endogenous genes is still not well understood. We have used a large number of existing chromosomal rearrangements in the Sex combs reduced homeotic gene to investigate the functions of the cis-acting elements within the endogenous gene. Characterization of the chromosomal rearrangements revealed that two genomic regions about 70 kb apart in the Sex combs reduced gene must be in cis to maintain proper repression. When not physically linked to each other, these genomic regions interact with regions on the homologous chromosome and cause derepression of its wild-type Sex combs reduced gene. Using a transgene assay, we have identified candidate fragments of DNA that may correspond to these regulatory genomic regions. Both regions appear to contain clusters of regulatory elements that can interact with elements on homologous chromosomes. We deleted two of these candidate elements from the endogenous Sex combs reduced gene by targetted gene replacement. Both deletions only partially disrupt silencing of the Sex combs reduced gene. This suggests that the elements in each cluster have partially redundant functions. Genetic studies identified the trithorax group of genes that are required for expression or function of the homeotic genes. Screening for mutations that interact with the trithorax group gene brahma (a subunit of the BRM chromatin-remodeling complexes), we isolated mutations in the rhinoceros gene. Rhinoceros encodes the Drosophila homolog of a human transcription factor that physically interacts with the von Hippel Lindau tumor suppressor protein. Loss of rhinoceros function causes a reduction in expression of the Sex combs reduced gene in the larval cells that form the adult first leg. Genetic studies also identified the Polycomb group of genes that are required for the transcriptional silencing of the homeotic genes. Screening for mutations that disrupt silencing, we have isolated mutations in many of the known Polycomb group genes and have identified several new genes that we are currently mapping. One of the genes that we have previously shown to be required for transcriptional silencing of the homeotic genes is the Mi-2 gene. During dirvergence of the genus Drosophila, part of the Mi-2 gene was duplicated to create the Chd3 gene. We have shown that Chd3 is not essential for either viability or fertility.